Feed-forward loop database
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The document describes a feed-forward loop (FFL) network motif. An FFL consists of two input transcription factors where one regulates the other and they jointly regulate a third gene. FFLs can have coherent or incoherent logic and either AND or OR logic. The document then discusses the structure and functions of FFLs, including how they can filter signals and respond to persistent stimuli. It also describes developing a database of FFLs to analyze regulatory networks.
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1) The document discusses the mechanisms of transcriptional control in eukaryotes. It describes the core promoter elements like TATA boxes and initiator elements that recruit RNA polymerase II.
2) General transcription factors help assemble the preinitiation complex at promoters and position the polymerase for transcription initiation. This involves sequential binding of factors like TFIID, TFIIB, and others.
3) The document outlines different classes of transcription factors that regulate gene expression, including those that contain zinc fingers, helix-turn-helix motifs, and leucine zippers, and how they bind DNA.SBML: What Is It About?
SBML: What Is It About?Mike Hucka
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SBML (Systems Biology Markup Language) is a format for representing computational models of biological processes. It defines data structures and serialization to XML for representing models in a neutral, machine-readable way. Development of SBML started in 2000 with the goal of facilitating exchange of models between software tools and databases. SBML provides syntax but limited semantics, so standard annotation schemes have been developed to link models to external data resources and provide additional meaning. The scope of SBML encompasses many types of biological models and is expanding through new packages to support additional model types.SBML (the Systems Biology Markup Language), model databases, and other resources
SBML (the Systems Biology Markup Language), model databases, and other resourcesMike Hucka
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The document provides an overview of the Systems Biology Markup Language (SBML), its features, and its importance for modeling biological processes. It outlines key concepts, resources for modelers, and emphasizes the need for reproducibility and interoperability in biological modeling. Additionally, it discusses upcoming developments in SBML standards and the significance of annotations for enhancing model communication.Gene regulatory networks
Gene regulatory networksMadiheh
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The document discusses gene regulatory networks (GRNs), including what they are, how they work, methods for modeling and analyzing them, and future challenges. Specifically, it notes that GRNs are networks of genes, proteins, and molecules that interact to control gene transcription. They respond to environmental signals and regulate processes like development. Computational models are needed to understand their complex behaviors under different conditions. Examples of models discussed include Boolean networks that represent gene expression levels as binary on/off states, continuous models that capture a range of expression levels, and stochastic models that account for random reactions.Lecture 6 (biol3600) transcription m rna processing- winter 2012 pw
Lecture 6 (biol3600) transcription m rna processing- winter 2012 pwPaula Faria Waziry
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This chapter discusses transcription in prokaryotes and eukaryotes. In prokaryotes, a single type of RNA polymerase binds to promoter sequences with the help of a sigma factor. Transcription proceeds through initiation, elongation, and termination. In eukaryotes, transcription requires chromatin remodeling and the binding of basal transcription factors that help recruit RNA polymerase to the promoter. RNA polymerase II synthesizes mRNA with the assistance of transcription factors that recognize regulatory promoter elements.Software for SBML Today
Software for SBML TodayMike Hucka
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The document discusses the Systems Biology Markup Language (SBML), which is used for representing computational models of biological processes through a simple and flexible encoding system. It covers various aspects of SBML, including its modeling capabilities, software tools, features, and the types of models it supports, as well as the results of a survey on SBML software tools. Additionally, it highlights the diversity and utility of SBML and acknowledges the contributions of various funding organizations.Ad
Feed-forward loop database
- 1. BACA THEODOR-STEFAN and SINIAVSCHI RADU MASTER ITEMS 2012 FEED-FORWARD LOOP CENTRAL DATABASE Based on the article: STRUCTURE AND FUNCTION OF THE FEED-FORWARD LOOP NETWORK MOTIF by S. Mangan and U. Alon
- 2. What is a FEED-FORWARD LOOP? Feed-forward loop (FFL) is a motif, consisting in a three-gene pattern composed of two input transcription factors. Each of the three interactions in the FFL can be either activating or repressing (coherent or incoherent). Simple regulation of Z by X and Y. Transcription factor X regulates transcription factor Y, and both jointly regulate Z. Sx and Sy are the inducers of X and Y, respectively. The action of X and Y is integrated at the Z promoter with a cis- regulatory input function , such as AND or OR logic.
- 3. FFL- Structure E. coli example:
- 4. COHERENT and INCOHERENT FFL type Decide from fluctuating signal Filter out pulses Respond to persistent stimulations Rapidly shut down Easly reverse Initially reacts strongly Later comes back to intermediate levels
- 5. FFL- Structure Logic function AND logic OR logic X and Y respond to external stimuli
- 6. Coherent Type-1 FFL AND logic Sx appear, X rapidly changes to X* X* binds to gene Z, but cannot activate it X* binds to gene Y, and begins to transcript it Z begins to be expressed after Ton time, when Y* crosses the activation threshold Kyz
- 8. MATERIALS AND METHODS Equations for Gene Regulation Reactions
- 9. MATERIALS AND METHODS Parameters for Functional FFLs
- 10. RESULTS
- 11. RESULTS
- 12. RESULTS
- 13. RESULTS
- 14. The FFL Database An user-friendly web app that integrates feed forward loops so scientists and other enthusiasts could use the results for educational and scientifical purposes.
- 15. The FFL Database An user-friendly web app that integrates feed forward loops so scientists and other enthusiasts could use the results for educational and scientifical purposes.
- 16. The actual FFL Database
- 17. Methods of FFL Database Search where we can get information about the regulatory networks Get from the information about the regulation by Transcription Factors. Construct an algorithm to extract the FFL motives different organisms regulatory networks. Make a hierarchical clasiffication of FFLs elements. Make a clasiffication acording to the origin of the signal that TFs sense. Search for differences betwen the data on each position of the FFLs making statistical tests to validate significance.
- 18. CONCLUSIONS Incoherent FFLs sign-sensitive accelerators. Coherent FFLs sign-sensitive delays. Some FFL occur more often than the others. Observe how TFs that detect different-origin signals compose Observe the dinamics on the TRN looking for the formation of specific topological structure, FFL Search for significative differences on the data by statistical tests on each position of the FFLs.
- 19. Thank you for your attention!